Haussmann, I. U., Dix, T. C., McQuarrie, D. W. J., Dezi, V., Hans, A. I., Arnold, R. and Soller M.(2024) Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts. Genome research 34: 2279-2292.
Evaluation of off-target effects in Drosophila:
Bian, W., Mcquarrie, D. W. J., Haussmann, I. U., Arnold, R. and Soller, M. (2025) Genetic evaluation of CRISPR-Cas9 off-target effects from deleterious mutations on Drosophila male single X chromosome. Functional & Integrative Genomics 25: 270-7.
Use of sgRNA/Cas9 for plasmid DNA scission in vitro is described here:
Haussmann, I. U., Ustaoglu, P., Brauer, U., Hemani, Y., Dix, T. and Soller, M. (2019) Plasmid-based gap-repair recombineered transgenes reveal a central role for introns in mutually exclusive alternative splicing of Down Syndrome Cell Adhesion Molecule exon 4. Nucleic Acid Research 47:1389-1403.
RNAFold from the ViennaRNA Package, web-server:RNA Fold
Lorenz, Ronny and Bernhart, Stephan H. and Honer zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L. ViennaRNA Package 2.0 Algorithms for Molecular Biology, 6:1 26, 2011, doi:10.1186/1748-7188-6-26
bpRNA script to interpret secondary structure files: BPRNA Database
Danaee, Padideh, et al. "bpRNA: large-scale automated annotation and analysis of RNA secondary structure." Nucleic acids research 46.11 (2018): 5381-5394.
https://doi.org/10.1093/nar/gky285
Cas-OFFinder: Cas-OFFinder, Version 2.4.: Bae S., Park J., & Kim J.-S. Cas-OFFinder: A fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 1473-1475 (2014).
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Zebrafish —
Database Center for Life Science (DBCLS)
,
CC BY 3.0
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Fly (Scaptomyza flava) —
MA Hanson
,
CC BY-SA 4.0
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Caenorhabditis elegans —
Database Center for Life Science (DBCLS)
,
CC BY 3.0
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Human silhouette —
Mette Aumala
,
CC0 (Public Domain)
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Arabidopsis thaliana —
Charles Andrès
,
CC BY-SA 3.0
- All others: Haussmann et al., Genome Research , Attribution-NonCommercial 4.0 International